Hello I am trying to call 'degree' on a graphNEL object and I get the following error using the example from the vignette. Thanks for your help -burak > library(graph) > set.seed(123) > g1 = randomEGraph(LETTERS[1:15], edges=100) > g1 A graphNEL graph with undirected edges Number of Nodes = 15 Number of Edges = 100 > > > nodes(g1) [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" > degree(g1) Error in degree(g1) : Not a graph object > > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] igraph_0.5.5-4 RBGL_1.30.1 org.Mm.eg.db_2.6.4 [4] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.16.18 [7] Biobase_2.14.0 graph_1.32.0 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] IRanges_1.12.6 tools_2.14.1 > [[alternative HTML version deleted]]

Hi Burak, You turned up a very odd bug. And a mysterious one. I just looked at the unit tests for degree, and they do not include exactly the case you used: a graphNEL returned by the randomEGraph method. But degree is successfully called on graphNEL's, and those tests run every day. Puzzling. Could you send me your g1 as an RData object? - Paul On Mar 12, 2012, at 10:29 AM, Burak Kutlu wrote: > Hello > I am trying to call 'degree' on a graphNEL object and I get the following error using the example from the vignette. > Thanks for your help > -burak > >> library(graph) >> set.seed(123) >> g1 = randomEGraph(LETTERS[1:15], edges=100) >> g1 > A graphNEL graph with undirected edges > Number of Nodes = 15 > Number of Edges = 100 >> >> >> nodes(g1) > [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" >> degree(g1) > Error in degree(g1) : Not a graph object >> >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] igraph_0.5.5-4 RBGL_1.30.1 org.Mm.eg.db_2.6.4 > [4] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.16.18 > [7] Biobase_2.14.0 graph_1.32.0 BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] IRanges_1.12.6 tools_2.14.1 >> > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Burak, On Mon, Mar 12, 2012 at 10:29 AM, Burak Kutlu <bkutlu at="" systemsbiology.org=""> wrote: > Hello > I am trying to call 'degree' on a graphNEL object and I get the following error using the example from the vignette. > Thanks for your help > -burak > >> library(graph) >> set.seed(123) >> g1 = randomEGraph(LETTERS[1:15], edges=100) >> g1 > A graphNEL graph with undirected edges > Number of Nodes = 15 > Number of Edges = 100 >> >> >> nodes(g1) > ?[1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" >> degree(g1) > Error in degree(g1) : Not a graph object >> Looks like you are hitting the degree() function in the igraph package. Try explicitly calling: graph::degree(g1) Dan >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 > ?[5] LC_MONETARY=en_US.UTF-8 ? ?LC_MESSAGES=en_US.UTF-8 > ?[7] LC_PAPER=C ? ? ? ? ? ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] igraph_0.5.5-4 ? ? ? ?RBGL_1.30.1 ? ? ? ? ? org.Mm.eg.db_2.6.4 > [4] RSQLite_0.11.1 ? ? ? ?DBI_0.2-5 ? ? ? ? ? ? AnnotationDbi_1.16.18 > [7] Biobase_2.14.0 ? ? ? ?graph_1.32.0 ? ? ? ? ?BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] IRanges_1.12.6 tools_2.14.1 >> > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor